SEED Academy, Spring 2012
Synthetic Biology
Homework #6
Due March 24, 2012
Individually
Go to the class website and navigate to the “Day 6” page on the Schedules tab. There you will find a list of four past iGEM projects, with links to the videos of their presentations at the iGEM Jamboree. There are also links to the PowerPoint slides, so you can follow along. Watch one of the four videos and answer these two questions:
Give a concise (1-2 sentence) description of what the engineered system does, with specific reference to what the system is physically/chemically doing to achieve its goal. (For example, “Cures cancer by repressing the activity of the Thingamabob gene in cancer cells”, rather than “Cures cancer”.)
What is/are the key part(s) of the biological system presented in the video? Look for the most important genes or proteins used in the design, especially ones that could not easily be swapped out for an equivalent part. (For example, in an arsenic-sensing bacterium, you might need a very specific membrane protein to sense arsenic, but the exact choice of inducible promoters in the system's internal logic might not matter as much.)
(Group assignment on the back...)
In Your Final Project Group
Choice!
Choose which of your three ideas you're going to develop into your final design project. Think about how feasible they are as projects and how important they are (the “what problem will this solve” question from the Three Ideas report), as well as how interesting they are.
The instructors will give each group a recommendation about which idea(s) we believe are most worth pursuing.
Specification
Write a specification for your system – a summary of what it is supposed to do, how it should interact with the outside world, how it should be used, etc. Write a few sentences for each of the questions below. (Where applicable, you may wish to present a few alternatives and discuss their pros and cons: e.g. a medical team could write about delivering their product as an injection, pill, probiotic yogurt...)
Your group should collaborate on this specification, splitting up research tasks amongst yourselves in order to get the work done. (It does not need to be one person per question!)
- What is the function of your system? Take your answer to the first question on the Three Ideas report, and get more detailed/specific. (Think back to the questions you answered for the iGEM video! You do not need to name particular genes or proteins you will use, but think about what specific physical, chemical, or molecular actions your system might perform on the outside world. Consult the instructors for advice on ways to tackle a thorny problem!)
- What information does your system need to take in from the outside world? (How does it know when to start/stop, when to produce a different level of output, etc?)
- How might your system be packaged and used by customers/patients? (Think about your target audience of users – do they need something easy and convenient, or can they work with tubes and micropipettors? Is your system single-use, multi-use, or intended to last a long time?)
- What are the safety considerations for your project? (Will it involve putting engineered cells inside people, or putting them in the environment, or just keeping them in a test tube? Think about how you might keep your cells from “escaping into the wild”.)